crossing96/oncoscreening huggingface dataset:
Immunohistochemical over-expression of HER2 does not always match with gene amplification in invasive bladder cancer.	BACKGROUND: HER2 is a potential target of therapy in urothelial cancer (UC). Pathological case stratification according to HER2 gene amplification or HER2 protein overexpression was critical for patients' selection in previous unsuccessful clinical trial with HER2 targeting agents. STUDY DESIGN: We evaluated the HER2 overexpression by immunohistochemistry (IHC) together with the amplification of the HER2 gene with chromogenic(CISH) and fluorescent (FISH) in situ hybridization in a cohort of 61 patients covering the whole spectrum of bladder UC variants, using a tissue microarray (TMA) approach. RESULTS: IHC was available in all the 61 cases while ISH in 37 and FISH in 42. At IHC, 2/61 cases (3%) were scored 3+; 2 (3%) scored 2+; 2 (3%) scored 1+; the remaining 55 (91%) scored 0. At CISH analysis 10/37 cases (27%) were amplified, 6 cases with HER2 amplification showed positive HER2 IHC (3+, 2+, 1+). Seven cases with IHC score 0 were amplified at CISH. FISH analysis revealed an amplification in 5/42 cases (12%). The total number of HER2amplified cases was different between chromogenic and fluorescent ISH with 5 cases amplified using FISH compared to 10 with CISH. CONCLUSIONS: In clinical trials with HER2 targeting agents the candidate patients should be investigated not only by IHC but also by ISH, independently of the IHC results. Since also usual type UC can overexpress HER2 we recommend to extend the patients' selection to all the histotypes of bladder cancer other than the micropapillary type.	bladder
Human Papillomavirus, MicroRNA and their Role in Cervical Cancer Progression, Diagnosis and Treatment Response: A Comprehensive Review.	Human Papillomavirus (HPV) is sexually transmitted and linked with vaginal, vulvar and cervix cancers in females, penile cancer in male, while anal and oropharyngeal cancer in both genders. Cervical cancer is ranked as third most identified cancer among females globally and is the fourth leading reason of cancer related mortality. The main aim of current study is to highlight the key role of miRNA in cervical cancer development, progression and their therapeutic responses. Current study entailed more than 50 PubMed cited articles related to miRNA role in cervical cancer. Studies have elucidated the role of miRNAs regulation in gene expression at post-transcriptional and translational level by targeting significant genes and therefore involved in cervical cancer. miRNAs control several cellular pathways involved in development of pre-malignant to metastatic stage and proliferation to malignancy. Current review elucidated and elaborated the key role of miRNA their application, treatment and therapeutic responses in cervical cancer.	bladder
Prediction of non-muscle-invasive bladder cancer recurrence during intravesical BCG immunotherapy by use of peripheral blood eosinophil count and percentage: a preliminary report.	OBJECTIVES: To determine whether there is an association between blood eosinophil count and percentage with the recurrence of nonmuscle invasive bladder cancer (NMIBC) during Bacillus Calmette-Guérin (BCG) maintenance therapy with our preliminary results. METHODS: A total of 53 patients with NMIBC underwent BCG immunotherapy between January 2015 and September 2018, and met our inclusion criteria were included in the study. The parameters age, gender, smoking status, comorbidity, blood neutrophil, lymphocyte and eosinophil counts, blood eosinophil percentage, previous single postoperative intravesical chemotherapy instillation, tumor characteristic, and total and maintenance dose numbers of BCG were extracted from our medical records and compared between patients with response and with recurrence. RESULTS: Blood eosinophil count and percentage were significantly higher in patients with recurrence compared to patients with response (0.263 ± 0.37 vs. 0.0134 ± 0.021, p = 0.01 and 0.31 ± 0.29 vs. 0.17 ± 0.27, p = 0.01). Other parameters were similar in patients with recurrence and response. Receiver-operating characteristic analysis showed a considerable diagnostic value of blood eosinophil count and percentage in the prediction of bladder cancer recurrence during BCG immunotherapy. CONCLUSION: Blood eosinophil count and percentage in patients with NMIBC can predict the disease recurrence during the BCG immunotherapy. Our research raised new questions and assumptions about the role of eosinophils during BCG immunotherapy.	bladder
Enhanced Quality and Effectiveness of Transurethral Resection of Bladder Tumour in Non-muscle-invasive Bladder Cancer: A Multicentre Real-world Experience from Scotland's Quality Performance Indicators Programme.	BACKGROUND: Clinical outcomes from non-muscle-invasive bladder cancer (NMIBC) are partly determined by the quality of initial interventions. To improve and standardise treatment for cancer, Scotland implemented a national Quality Performance Indicator (QPI) programme for bladder cancer (BC). OBJECTIVE: To evaluate compliance with specific quality indicators (QIs) related to transurethral resection of bladder tumour (TURBT) and to understand clinical outcomes from NMIBC following the introduction of the QPI programme. DESIGN, SETTING, AND PARTICIPANTS: Within a robust governance framework, 12 mandatory evidence-based QPIs were implemented nationally in April 2014. We report prospectively collected data for all new BC patients (between April 2014 and March 2017). We include follow-up data for 2689 patients. INTERVENTION: The TURBT-related QPIs were (1) using a bladder diagram, (2) single post-TURBT instillation of mitomycin C (SPI-MMC), (3) detrusor muscle (DM) in the specimen, and (4) early re-TURBT in high-risk NMIBC. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We measured compliance with these QPIs and (1) recurrence rate at first follow-up cystoscopy (RRFFC), (2) rates of residual cancer, and (3) pT2 cancer at re-TURBT. Associations between QPI compliance, tumour features, and outcomes were assessed with multivariable logistic regression models. RESULTS AND LIMITATIONS: Among 4246 new BC patients, SPI-MMC was used in 67% (2029/3023) NMIBC patients. In 1860 NMIBC patients undergoing TURBT, RRFFC, rate of residual cancer, and rate of pT2 at re-TURBT were 13% (116/888), 33% (212/653), and 2.9% (19/653), respectively. SPI-MMC was associated with lower RRFFC, independent of all variables including hospital volume and surgeon. Presence of DM in the specimen halved the likelihood of residual disease in pT1 cancers. The main limitation is the lack of a pre-QPI introduction cohort for comparison. CONCLUSIONS: The implementation of a QI programme in Scotland appears to facilitate high-quality TURBT, which in a real-world setting is associated with low early recurrence/residual cancer and accurate pathological staging. PATIENT SUMMARY: Following the first 3 yr of implementing a novel Quality Performance Indicator (QPI) programme in Scotland, we assessed compliance and outcomes in non-muscle-invasive bladder cancer. Evaluating over 4000 new bladder cancer patients, we found that the QPI programme was associated with low recurrence and accurate staging following the initial transurethral resection of bladder tumour.	bladder
Quantitative Analysis of Enhanced Computed Tomography in Differentiating Cystitis Glandularis and Bladder Cancer.	OBJECTIVE: This study was performed to assess the value of quantitative analysis of enhanced computed tomography (CT) values in the differential diagnosis of bladder cancer and cystitis glandularis (CG). METHODS: Eighty patients with bladder masses (39 with CG and 41 with bladder cancer) who underwent enhanced CT were retrospectively reviewed. The CT enhancement values of the lesion and normal bladder wall in the arterial phase, venous phase, and delayed phase were measured. The relative enhancement CT values (relative enhancement CT value = enhancement CT value of lesion - enhancement CT value of normal bladder) in the arterial phase, venous phase, and delayed phase were also calculated. The pathological results were used as the gold standard, and the area under the curve (AUC), sensitivity, and specificity were calculated for the six groups of quantitative indicators (enhanced CT values and relative enhanced CT values of CG and bladder cancer in the arterial, venous, and delayed phases). We performed the leave-group-out cross-validation method to validate the accuracy, AUC, sensitivity, and specificity. The differences in accuracy, AUC, sensitivity, and specificity among the six groups of quantitative indicators were compared by the t-test. RESULTS: In a combined analysis of the AUC, sensitivity, and specificity performance, the best indicator was the arterial-phase relative enhancement CT value with a cut-off of 25.85 HU (AUC, 0.966; sensitivity, 95.1%; specificity, 92.3%). We used the 100-times leave-group-out cross-validation method to validate the accuracy, AUC, sensitivity, and specificity. Arterial-phase relative enhancement CT values showed the highest AUC and accuracy among the six groups, with statistical significance (P < 0.05). CONCLUSION: Quantitative analysis of enhanced CT is of great clinical value in the differential diagnosis of CG and bladder cancer.	bladder
Oncological outcome according to attainment of pentafecta after robot-assisted radical cystectomy in patients with bladder cancer included in the multicentre KORARC database.	OBJECTIVES: To investigate the oncological significance of a robot-assisted radical cystectomy (RARC)-related pentafecta in patients with bladder cancer. PATIENTS AND METHODS: Using the KORARC database, which includes data from 12 centres, data from 730 patients who underwent RARC between April 2007 and May 2019 were prospectively collected and retrospectively analysed. Pentafecta was achieved if patients met all of the following criteria: (i) negative soft tissue surgical margin; (ii) ≥16 lymph nodes removed; (iii) no major complications (Clavien-Dindo grade 3-5) within 90 days; (iv) no clinical recurrence within the first 12 months; and (v) no ureteroenteric stricture. Patients were divided into two groups according to pentafecta attainment, and a comparison of overall survival (OS) and cancer-specific survival (CSS) using multivariate Cox proportional analysis was then carried out. RESULTS: Of the 730 patients included in this analysis, 208 (28.5%) attained the RARC pentafecta; the remaining 522 (71.5%) did not. The mean age of the patients was 64.67 years, 85.1% were men, 53.6% received a conduit, 37.7% received orthotopic neobladders and the total complication rate was 57.8%. Those who attained the pentafecta received more neobladders (P = 0.039), were more likely to be treated with the intracorporeal technique (P < 0.001), had longer operating times (P = 0.020) and had longer console time (P = 0.021) compared with those who did not attain the pentafecta. Over a mean of 31.1 months of follow-up, the pentafecta attainment group had significantly higher OS and CSS rates compared with the non-attainment group (10-year OS 70.4% vs 58.1%, respectively [P = 0.016]; 10-year CSS 87.8% vs 70.0%, respectively [P = 0.036]). Multivariate analysis showed that the RARC pentafecta was a significant predictor of overall mortality (hazard ratio 0.561; P = 0.038). CONCLUSIONS: Patients who attained the RARC pentafecta had significantly better survival outcomes compared with those who did not. These criteria could be used to standardize assessment of the surgical quality of RARC. In the future, a similar study using an independent cohort is warranted to confirm our results.	bladder
Histopathological distinction of non-invasive and invasive bladder cancers using machine learning approaches.	BACKGROUND: One of the most challenging tasks for bladder cancer diagnosis is to histologically differentiate two early stages, non-invasive Ta and superficially invasive T1, the latter of which is associated with a significantly higher risk of disease progression. Indeed, in a considerable number of cases, Ta and T1 tumors look very similar under microscope, making the distinction very difficult even for experienced pathologists. Thus, there is an urgent need for a favoring system based on machine learning (ML) to distinguish between the two stages of bladder cancer. METHODS: A total of 1177 images of bladder tumor tissues stained by hematoxylin and eosin were collected by pathologists at University of Rochester Medical Center, which included 460 non-invasive (stage Ta) and 717 invasive (stage T1) tumors. Automatic pipelines were developed to extract features for three invasive patterns characteristic to the T1 stage bladder cancer (i.e., desmoplastic reaction, retraction artifact, and abundant pinker cytoplasm), using imaging processing software ImageJ and CellProfiler. Features extracted from the images were analyzed by a suite of machine learning approaches. RESULTS: We extracted nearly 700 features from the Ta and T1 tumor images. Unsupervised clustering analysis failed to distinguish hematoxylin and eosin images of Ta vs. T1 tumors. With a reduced set of features, we successfully distinguished 1177 Ta or T1 images with an accuracy of 91-96% by six supervised learning methods. By contrast, convolutional neural network (CNN) models that automatically extract features from images produced an accuracy of 84%, indicating that feature extraction driven by domain knowledge outperforms CNN-based automatic feature extraction. Further analysis revealed that desmoplastic reaction was more important than the other two patterns, and the number and size of nuclei of tumor cells were the most predictive features. CONCLUSIONS: We provide a ML-empowered, feature-centered, and interpretable diagnostic system to facilitate the accurate staging of Ta and T1 diseases, which has a potential to apply to other types of cancer.	bladder
Glucose promotes epithelial-mesenchymal transitions in bladder cancer by regulating the functions of YAP1 and TAZ.	Glucose levels and type 2 diabetes (T2D) are both associated with tumorigenesis and epithelial-mesenchymal transitions (EMTs). EMTs facilitate bladder cancer (BC) metastasis development, but the mechanism by which high-glucose levels promote these EMTs in BC remains unclear. Therefore, we sought to elucidate the mechanism underlying EMT promotion due to increased glucose levels. T24 and UMUC-3 cells were cultured in media containing different glucose concentrations. YAP1, TAZ, GLUT1 and EMT-associated marker expression was analysed via Western blotting and qPCR. BC cell proliferation and invasion were assessed using MTT and Transwell assays, respectively. A xenograft nude mouse model of diabetes was used to evaluate tumour growth and metastasis in vivo. T2D was positively associated with pathologic grade (P = .016) and TNM stage (P < .001) in BC. High glucose triggered BC cell proliferation and invasion in both in vitro and in vivo conditions. High-glucose levels also promoted EMTs in BC cells and increased YAP1 and TAZ expression. YAP1 or TAZ knockdown altered EMT marker expression and decreased GLUT1 expression. Overall, our results suggest that high-glucose levels promote EMTs in BC cells via YAP1 and TAZ regulation. These effector molecules may be promising therapeutic targets for BC cases comorbid with T2D.	bladder
Trained immunity as a molecular mechanism for BCG immunotherapy in bladder cancer.	Intravesical BCG instillation is the gold-standard adjuvant immunotherapy for patients with high-risk non-muscle-invasive bladder cancer. However, the precise mechanism of action by which BCG asserts its beneficial effects is still unclear. BCG has been shown to induce a non-specific enhancement of the biological function in cells of the innate immune system, creating a de facto heterologous immunological memory that has been termed trained immunity. Trained immunity or innate immune memory enables innate immune cells to mount a more robust response to secondary non-related stimuli after being initially primed (or trained) by a challenge such as BCG. BCG-induced trained immunity is characterized by the metabolic rewiring of monocyte intracellular metabolism and epigenetic modifications, which subsequently lead to functional reprogramming effects, such as an increased production of cytokines, on restimulation. Results from BCG vaccination studies in humans show that trained immunity might at least partly account for the heterologous beneficial effects of BCG vaccination. Additionally, immunity might have a role in the effect of BCG immunotherapy for bladder cancer. Based on these indications, we propose that trained immunity could be one of the important mechanisms mediating BCG immunotherapy and could provide a basis for further improvements towards a personalized approach to BCG therapy in non-muscle-invasive bladder cancer.	bladder
Identification of cell division cycle 20 as a candidate biomarker and potential therapeutic target in bladder cancer using bioinformatics analysis.	PURPOSE: As bladder cancer (BC) is very heterogeneous and complicated in the genetic level, exploring genes to serve as biomarkers and therapeutic targets is practical. MATERIALS AND METHODS: We searched Gene Expression Omnibus (GEO) and downloaded the eligible microarray datasets. After intersection analysis for identified differentially expressed genes (DEGs) of included datasets, overlapped DEGs were identified and subsequently analyzed with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein-Protein Interaction (PPI) and hub genes identification. Hub genes were further analyzed with mRNA expression comparation in Oncomine and Gene Expression Profiling Interactive Analysis (GEPIA) database, proteomics-based validation in The Human Protein Atlas (THPA) and survival analysis in GEO and Oncolnc database. RESULTS: We analyzed five eligible GEO datasets and identified 76 overlapped DEGs mapped into PPI network with 459 edges which were mainly enriched in cell cycle pathway and related terms in GO and KEGG analysis. Among five identified hub genes, which are Cyclin-Dependent Kinase 1 (CDK1), Ubiquitin-Conjugating Enzyme E2 C (UBE2C), Cell Division Cycle 20 (CDC20), Microtubule Nucleation Factor (TPX2) and Cell Division Cycle Associated 8 (CDCA8); CDC20 and CDCA8 were confirmed as significant in mRNA expression comparation and proteomics-based validation. However, only CDC20 was considered prognostically significant in both GEO and Oncolnc database. CONCLUSIONS: CDC20 and CDCA8 were identified as candidate diagnostic biomarkers for BC in the present study; however, only CDC20 was validated as prognostically valuable and may possibly serve as a candidate prognostic biomarker and potential therapeutic target. Still, further validation studies are essential and indispensable.	bladder
Müllerianosis of the urinary bladder with unilateral complete renal agenesis: a rare coincidental finding causing delayed presentation.	Müllerianosis is a rare benign lesion of the urinary bladder, which is constituted by two or more of the Müllerian-duct-derived tissues. We report a 45-year-old perimenopausal multiparous woman presenting with occasional episodes of dysuria and lower abdominal discomfort of recent duration. Ultrasound examination revealed a well-defined lesion in urinary bladder and the absence of left kidney. Contrast-enhanced CT of the abdomen confirmed the findings. During diagnostic cystoscopy, haemorrhagic polypoidal lesions were noted in the left side of the posterolateral wall and dome of urinary bladder along with the absence of left ureteric orifice. Transurethral resection of the bladder lesions was done and histology examination confirmed the diagnosis of Müllerianosis. She was administered Luteinizing hormone-releasing hormone (LHRH) agonist monthly. At 1 year of follow-up, cystoscopy showed only scar tissue. The case was reported for the rarity of Müllerianosis noted in a patient with unilateral agenesis of kidney, a possible cause of delayed presentation.	bladder
A novel LncRNA transcript, RBAT1, accelerates tumorigenesis through interacting with HNRNPL and cis-activating E2F3.	BACKGROUND: Long non-coding RNAs (lncRNAs) have been identified as important epigenetic regulators that play critical roles in human cancers. However, the regulatory functions of lncRNAs in tumorigenesis remains to be elucidated. Here, we aimed to investigate the molecular mechanisms and potential clinical application of a novel lncRNA, retinoblastoma associated transcript-1 (RBAT1), in tumorigenesis. METHODS: RBAT1 expression was determined by real-time PCR in both retinoblastoma (Rb) and bladder cancer (BCa) cell lines and clinical tissues. Chromatin isolation using RNA purification (ChIRP) assays were performed to identify RBAT1-interacting proteins. Patient-derived xenograft (PDX) retinoblastoma models were established to test the therapeutic potential of RBAT1-targeting GapmeRs. RESULTS: Here, we found that RBAT1 expression was significantly higher in Rb and BCa tissues than that in adjacent tissues. Functional assays revealed that RBAT1 accelerated tumorigenesis both in vitro and in vivo. Mechanistically, RBAT1 recruited HNRNPL protein to E2F3 promoter, thereby activating E2F3 transcription. Therapeutically, GapmeR-mediated RBAT1 silencing significantly inhibited tumorigenesis in orthotopic xenograft retinoblastoma models derived from Rb cell lines and Rb primary cells. CONCLUSIONS: RBAT1 overexpression upregulates a known oncogene, E2F3, via directly recruiting HNPNPL to its promoter and cis-activating its expression. Our finding provides a novel mechanism of lncRNA biology and provides potential targets for diagnosis and treatment of Rb and BCa.	bladder
Systemic treatment for advanced urothelial cancer: an update on recent clinical trials and current treatment options.	After cisplatin-based chemotherapy became the standard treatment for metastatic urothelial cancer (mUC), very little progress has been made in the treatment landscape of this condition until recently. With increased knowledge about the molecular biology of mUC and advances in the field of cancer immunobiology, there has been an explosion in the number of clinical trials for mUC, and systemic treatment of mUC is rapidly changing. Despite the availability of several novel therapeutic agents, cisplatin-based cytotoxic chemotherapy remains the standard, first-line treatment option. Immune checkpoint inhibitors (ICIs), including programmed death-1 and programmed death ligand-1 inhibitors, are preferred second-line treatment options that are also used in first-line cisplatin-ineligible settings. For patients with actionable fibroblast growth factor receptor 2 (FGFR2) or FGFR3 genomic alterations, erdafitinib can be considered after platinum-based treatment. Enfortumab vedotin, a monoclonal antibody targeting nectin-4 conjugated to monomethyl auristatin E, has been approved for patients who do not respond to both cytotoxic chemotherapy and ICIs. In this review, we address the clinical trial data that have established the current standard treatments and ongoing clinical trials of various agents with different mechanisms as well as provide a brief overview of current practice guidelines and recommendations in patients with mUC.	bladder